Workflow: preprocess_vcf.cwl
Fetched 2024-04-19 00:20:12 GMT
Verified with cwltool version 3.1.20221201130942
This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| ref | File |
Reference file, used for normalized INDELs |
|
| vcfdir | Directory |
The directory where the files are |
|
| out_dir | String |
The name of the output directory |
|
| filesToPreprocess | String[] |
The files to process |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter_for_indel |
preprocess_vcf.cwl#filter_for_indel/b5aa1c6a-fdc6-480c-9689-d67e7fbe7b4e
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/507b2bf7-aeea-4a48-8c75-98975fdbeff2
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/88dca120-b9b3-4772-97e5-c844c41c41da
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/dc46a552-1ac6-4747-99cc-87b6cccbcbb2
(ExpressionTool)
|
||
| gather_clean_vcfs |
preprocess_vcf.cwl#gather_clean_vcfs/de8e3a8c-51a8-4ff8-a2a7-9b5d3ac8040d
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/ca40d46e-be33-4374-8890-b0fcc72d0b11
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/e5c8a510-2762-485b-b5e9-221f2e0848c4
(ExpressionTool)
|
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| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/27383e9b-6b5c-4da2-9bc5-2af048e7333e
(ExpressionTool)
|
||
| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/611bffeb-7bc3-4c6a-bd25-0b2d99604f48
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/17af1cb5-c76c-4f27-92f9-588dab10c9b5
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/85884bbd-de02-4f80-aa04-dbd02d0145a9
(ExpressionTool)
|
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| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/5d716123-675c-4011-9e9e-7f52f1fd83b2
(ExpressionTool)
|
||
| populate_output_record |
preprocess_vcf.cwl#populate_output_record/586b5816-e1a9-41d7-91c5-e938d4956ee2
(ExpressionTool)
|
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| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/62545747-42bd-425f-b1db-7b87b7966112
(ExpressionTool)
|
||
| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/ee904001-84d6-40a2-93be-cc74711921f4
(ExpressionTool)
|
||
| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/7bea6dce-d1b4-46c6-8d51-57dc001c42d9
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/b38a8a4785746b8267913ea5389e21ae6dc921a3/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/b38a8a4785746b8267913ea5389e21ae6dc921a3/preprocess_vcf.cwl
